X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=580eea44599ed2541ddc699cd17a09717d1b8aaf;hb=ebaa3f63d0dc201b9b5a5cd91e2cfa3c7157f143;hp=4f1073c641064406ee3db9b2907ec711a4da3e69;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 4f1073c..580eea4 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -6,7 +6,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either @@ -16,7 +16,7 @@ // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. -// +// // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -71,21 +71,21 @@ import org.forester.surfacing.DomainId; import org.forester.surfacing.DomainLengthsTable; import org.forester.surfacing.DomainParsimonyCalculator; import org.forester.surfacing.DomainSimilarity; +import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring; +import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField; import org.forester.surfacing.DomainSimilarityCalculator; +import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; import org.forester.surfacing.GenomeWideCombinableDomains; +import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder; import org.forester.surfacing.MappingResults; import org.forester.surfacing.PairwiseDomainSimilarityCalculator; import org.forester.surfacing.PairwiseGenomeComparator; import org.forester.surfacing.PrintableDomainSimilarity; +import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; import org.forester.surfacing.Protein; import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator; import org.forester.surfacing.Species; import org.forester.surfacing.SurfacingUtil; -import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring; -import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField; -import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; -import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder; -import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; import org.forester.util.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; @@ -522,9 +522,11 @@ public class surfacing { ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" ); } if ( intree.getNumberOfExternalNodes() < number_of_genomes ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "number of external nodes [" - + intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file - + "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "number of external nodes [" + intree.getNumberOfExternalNodes() + + "] of input tree [" + intree_file + + "] is smaller than the number of genomes the be analyzed [" + + number_of_genomes + "]" ); } final StringBuilder parent_names = new StringBuilder(); final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names ); @@ -1304,8 +1306,8 @@ public class surfacing { .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " - + e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "cannot read secondary features map file: " + e.getMessage() ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file [" @@ -1778,8 +1780,7 @@ public class surfacing { if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { parser.setMaxAllowedOverlap( max_allowed_overlap ); } - parser - .setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); + parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); if ( individual_score_cutoffs != null ) { parser.setIndividualScoreCutoffs( individual_score_cutoffs ); } @@ -1813,7 +1814,8 @@ public class surfacing { System.out.println( "Domains ignored due to individual score cutoffs: " + parser.getDomainsIgnoredDueToIndividualScoreCutoff() ); log( "Domains ignored due to individual score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer ); + + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), + log_writer ); System.out.println( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval() ); log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer ); @@ -1829,7 +1831,8 @@ public class surfacing { System.out.println( "Domains ignored due negative domain filter : " + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); log( "Domains ignored due negative domain filter : " - + parser.getDomainsIgnoredDueToNegativeDomainFilter(), log_writer ); + + parser.getDomainsIgnoredDueToNegativeDomainFilter(), + log_writer ); System.out.println( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap() ); log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(), @@ -2082,12 +2085,13 @@ public class surfacing { } SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() .get( 0 ) ); @@ -2119,14 +2123,19 @@ public class surfacing { jacknife_resamplings, jacknife_ratio, random_seed ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + "_" + + ForesterUtil.round( jacknife_ratio, 2 ) + + "_" + + jacknife_resamplings + + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 ) + + "_" + jacknife_resamplings + + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); // if ( infer_species_trees ) { // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc